ArticleBMC cancer2022
Uncovering potential genes in colorectal cancer based on integrated and DNA methylation analysis in the gene expression omnibus database.
Article in BMC cancer, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 13 citations in OpenAlex.
- Metastasis-associated DNA methylation alterations persist after accounting for immune and stromal cell heterogeneity in primary colorectal tumors.Research square · 2026Article
- Rank-dependent control of tuft and BEST4 cell development in the intestine.Nature communications · 2026Article
- Impact of treatment history on drug resistance of metastatic colorectal cancer organoids.iScience · 2025Article
- Multifaceted role of serine hydroxymethyltransferase in health and disease.Molecules and cells · 2025Review
- Cancer pharmacoinformatics: Databases and analytical tools.Functional & integrative genomics · 2024Review
- Tissue-specific atlas of trans-models for gene regulation elucidates complex regulation patterns.BMC genomics · 2024Article
- The Expression of the Claudin Family of Proteins in Colorectal Cancer.Biomolecules · 2024Review
- CDH3 Is an Effective Serum Biomarker of Colorectal Cancer Distant Metastasis Patients.Journal of Cancer · 2024Article
- Multi-Omics Data Analysis Identifies Prognostic Biomarkers across Cancers.Medical sciences (Basel, Switzerland) · 2023Article
- Article
- High VSX1 expression promotes the aggressiveness of clear cell renal cell carcinoma by transcriptionally regulating FKBP10.Journal of translational medicine · 2022Article
- Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundColorectal cancer (CRC) is major cancer-related death. The aim of this study was to identify differentially expressed and differentially methylated genes, contributing to explore the molecular mechanism of CRC.
methodsFirstly, the data of gene transcriptome and genome-wide DNA methylation expression were downloaded from the Gene Expression Omnibus database. Secondly, functional analysis of differentially expressed and differentially methylated genes was performed, followed by protein-protein interaction (PPI) analysis. Thirdly, the Cancer Genome Atlas (TCGA) dataset and in vitro experiment was used to validate the expression of selected differentially expressed and differentially methylated genes. Finally, diagnosis and prognosis analysis of selected differentially expressed and differentially methylated genes was performed.
resultsUp to 1958 differentially expressed (1025 up-regulated and 993 down-regulated) genes and 858 differentially methylated (800 hypermethylated and 58 hypomethylated) genes were identified. Interestingly, some genes, such as GFRA2 and MDFI, were differentially expressed-methylated genes. Purine metabolism (involved IMPDH1), cell adhesion molecules and PI3K-Akt signaling pathway were significantly enriched signaling pathways. GFRA2, FOXQ1, CDH3, CLDN1, SCGN, BEST4, CXCL12, CA7, SHMT2, TRIP13, MDFI and IMPDH1 had a diagnostic value for CRC. In addition, BEST4, SHMT2 and TRIP13 were significantly associated with patients' survival.
conclusionsThe identified altered genes may be involved in tumorigenesis of CRC. In addition, BEST4, SHMT2 and TRIP13 may be considered as diagnosis and prognostic biomarkers for CRC patients.
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